Open Access Highly Accessed Research article

Alternative splicing and differential gene expression in colon cancer detected by a whole genome exon array

Paul J Gardina, Tyson A Clark, Brian Shimada, Michelle K Staples, Qing Yang, James Veitch, Anthony Schweitzer, Tarif Awad, Charles Sugnet, Suzanne Dee, Christopher Davies, Alan Williams and Yaron Turpaz*

Author Affiliations

Affymetrix, Inc., 3420 Central Expressway, Santa Clara, CA 95051, USA

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BMC Genomics 2006, 7:325  doi:10.1186/1471-2164-7-325

Published: 27 December 2006

Additional files

Additional file 1:

Table_A1_differential_CORE_genes. Genes in the Core metaprobe set which are differentially regulated in colon cancer. The log fold change is shown for Normal relative to Tumor samples, which is negative for up-regulated genes. "Cancer" Indicates that the gene has been implicated in various cancers. Question marks indicate an unproven association. "CRC" indicates that the gene has been implicated specifically in colon or colorectal cancer. Gene annotations are according to the Affymetrix file HuEx-1_0-st-transcript-annot.csv (NCBI build 35, UCSC hg17). Abbreviations: Exc., extracellular; proc., processing; R & R, recombination and repair.

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Additional file 2:

Table_A2_differential_FULL_genes. Genes in the Full metaprobe set which are differentially regulated in colon cancer. Transcript IDs and gene annotations are according to the Affymetrix file HuEx-1_0-st-transcript-annot.csv (NCBI build 35, UCSC hg17). Genes which are also present in the Core list are omitted. "Support" indicates genes that have prior either annotation ("A") or a transcript expression exceeding a threshold PLIER signal of 15 in 50% of the samples in at least one tissue type ("E").

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Additional file 3:

Table_A3_AS_200Candidates. Top scoring candidates for alternative splicing events. This list was obtained by a) filtering exons with DABG at 0.05, b) filtering genes at a signal threshold of 70, c) requiring an log ratio > 0.5, d) a Splicing Index p-value < 0.005 and e) only Core exons (Note that the list extends to the top 200 events that were used for comparison to bioinformatic EST methods). The Exon ID and Gene ID are the Affymetrix probeset IDs and transcript cluster IDs, respectively. Log mean difference is the logged ratio of the exon signal from each tissue after normalization to gene-level signals in each tissue. SI p-value is derived from the Splicing Index t-test.

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Additional file 4:

Table_A4_PCR_primers. Primers and summary of PCR results for splicing candidates and previously reported splicing events in colon cancer. Forward and Reverse are the exon locations of the validation PCR primers. "Known Alternative Splicing Events" were determined from RefSeq, full length mRNAs and ESTs on the UCSC Genome Browser. "Result" indicates the interpretation of the PCR result ("NC", No change in alternative splicing between the two tissue types; "No", no alternative splicing observed; "GE", differences attributed to different levels of gene expression in the two tissue types). Abbreviations: Ex, exon; CE, cassette exon; MEE, mutually exclusive exon; Alt., alternative.

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Additional file 5:

Table_A5_PCR_densitometry. Analysis of densitometric scan data from PCR validation gels.

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